Biology B242: Evolutionary and Ecological Genetics Exam 2000

Total Page：16

File Type：pdf, Size：1020Kb

BIOLOGY B242: EVOLUTIONARY AND ECOLOGICAL GENETICS EXAM 2000 Answer ONE question from section A, TWO questions from section B, and ALL OF section C (overleaf). Each section carries 1/3 of the marks on the paper. SECTION A. Answer ONE of questions 1-3. 1. Consider, using specific cases, whether evolutionary biologists in the year 2000 need to invoke different genetic processes to account for micro- and macro-evolution? 2. Are the effects of mutation on fitness important in evolution? Support your argument with suitable examples. 3. “Every species has come into existence coincident both in space and time with a pre- existing closely allied species” (Wallace 1855). Discuss this statement in the light of modern theories of spatial evolution. SECTION B. Answer TWO of questions 4-8. 4. What are the relative merits of the phylogenetic and cladistic approaches to resolving the classification of species? Assess the assumptions of each method in your answer. 5. How does genetic drift interact with selection in (a) chromosomal evolution OR (b) survival of endangered populations? 6. Is artificial selection a useful tool for an evolutionary biologist? Give some examples of its use to illustrate your response. 7. What are secondary sexual characteristics? What best explains them? 8. What use is linkage disequilibrium in modern evolutionary genetics? Remember to answer Section C overleaf! TURN OVER SECTION C. Attempt ALL parts of question 9. 9. Dobzhansky studied the frequency of inversions “Standard” and “Arrowhead” in two mountain peak populations of Drosophila pseudoobscura in California 50 km apart: Inversion Arrowhead Arrowhead/Standard Standard Genotype Homozygotes Heterozygotes Homozygotes Kingston Peak 52 39 12 Charleston Peak 102 21 5 a) Estimate the frequencies of Standard and Arrowhead in each population. b) Calculate the expected genotype frequencies for each population. c) Use a chi-square test to find whether there is any evidence for deviation from Hardy- Weinberg in each population. d) How might you explain your findings in part (c) given the data so far? e) In addition: (i) It is known that the local effective population sizes of each peak were very large, well over 1000 flies per peak, and that mating is approximately random. (ii) Dobzhansky found that environmental conditions on different mountains contribute to geographic variation in inversion frequency; (iii) Jones has since found that some D. pseudoobscura individuals regularly move over 60km between sites. (iv) Dobzhansky showed that inversion frequencies in laboratory populations stabilize at about 65% Arrowhead: 35% Standard. How do these observations (i-iv) compare with the genotype frequency data from Kingston Peak and Charleston Peak? How might these observations be reconciled? Can you suggest any experiments to test between your hypotheses? END OF PAPER .

Copy Link

Recommended publications

Qrup: 127E; Fənn: Ecological Genetics İmtahan Sualları (2021-Ci Il, Tədris Yükü (Saat) Cəmi: 90 Saat; Mühazirə 45 Saat; Məşğələ 45 Saat)
Bakı Dövlət Universiteti Biologiya fakültəsi; Qrup: 127E; Fənn: Ecological genetics İmtahan sualları (2021-ci il, tədris yükü (saat) cəmi: 90 saat; mühazirə 45 saat; məşğələ 45 saat) 1. The subject of Ecological genetics, its main problems 2. The theoretical and practical problems of Ecological genetics 3. Brief history of Ecological genetics 4. The investigation methods of Ecological genetics 5. Conception of adaptation, adaptive reaction norm 6. The role of modifications and genotypic variations in adaptation 7. Different types of adaptations 8. Ontogenetic and phylogenetic adaptations 9. Population-species adaptations and adaptations in biogeocenosis 10. Adaptive traits of biological systems: plasticity, flexibility, stability, homeostasis, genetic homeostasis and canalization 11. Genetic diversity, its types; significance of conservation of genetic diversity 12. Genetic erosion, its causes and results 13. Genetic effects of population fragmentation, population size, inbreeding and gene flow 14. Population bottleneck and fonder effect 15. Conservation methods of genetic diversity 16. Evolution as a consequence of changes in alleles and allele frequencies in populations over time 17. Factors affecting allele frequencies and genetic equilibrium in populations 18. Genetic nature of adaptive reactions 19. Role of heterozygosity and polymorphism in adaptation 20. Explaining the high level of genetic variation in populations 21. Detecting genetic variation by artificial selection and genetic markers 22. Polymerase chain reaction (PCR); its steps, limits, types and applications 23. Integration of adaptive reactions 24. Role of supergenes and gene-complexes in adaptation 25. Heterostyly, its role in adaptation 26. Genetic regulation mechanisms of adaptive traits 27. Effects of environmental factors on gene expression in prokaryotes; the operon model of regulation 28.
[Show full text]
Ecological Genetics of Freshwater Fish: a Short Review of the Genotype–Phenotype Connection
Animal Biodiversity and Conservation 34.2 (2011) Review309 Ecological genetics of freshwater fish: a short review of the genotype–phenotype connection O. Vidal & J. L. García–Marín Vidal, O. & García–Marín, J. L., 2011. Ecological genetics of freshwater fish: a short review of the genotype– phenotype connection. Animal Biodiversity and Conservation, 34.2: 309–317. Abstract Ecological genetics of freshwater fish: a short review of the genotype–phenotype connection.— Molecular eco- logy or ecological genetics is an expanding application of population genetics which has flourished in the last two decades but it is dominated by systematic and phylogeographic studies, with relatively little emphasis on the study of the genetic basis of the process of adaptation to different ecological conditions. The relationship between genotype and adaptive phenotypes is weak because populations are often difficult to quantify and experiments are logistically challenging or unfeasible. Interestingly, in freshwater fish, studies to characterize the genetic architecture of adaptive traits are not as rare as in other vertebrate groups. In this review, we summarize the few cases where the relationship between the ecology and genetics of freshwater fish is more developed, namely the relationship between genetic markers and ecological phenotypes. Key words: Ecological genetics, Molecular ecology, Genotype–phenotype relationship, Adaptation, Landscape genetics, Species introduction. Resumen Genética ecológica de los peces de agua dulce: una breve revisión de la conexión genotipo–fenotipo.— La ecología molecular o la genética ecológica es una aplicación de la genética de poblaciones que durante las dos últimas décadas ha sufrido un proceso de expansión. Sin embargo, en la ecología molecular predominan los estudios sistemáticos y filogeográficos, con relativamente poco énfasis en el análisis de la base genética del proceso de adaptación a diferentes condiciones ecológicas.
[Show full text]
IB 162 Ecological Genetics University of California, Berkeley Department of Integrative Biology (4 Units)
Ecological Genetics Integrative Biology 162 IB 162 Ecological Genetics University of California, Berkeley Department of Integrative Biology (4 units) Course Description: This course presents modern approaches to studying evolution in natural populations, which requires both ecology and genetics. We will study quantitative and molecular causes of inheritance of ecologically important traits and their evolution. We will use simple mathematical models to predict evolution in natural populations. This course will help you build a conceptual framework for understanding biology. "Nothing in biology makes sense except in the light of evolution." . Theodosius Dobzhansky (1970) Genetics of the Evolutionary Process Format: There are lecture and discussion sessions. Lectures will focus primarily on broad concepts and ideas. Weekly discussion sections will help you master ideas and give you practice in reading and analyzing primary scientific literature. Lectures: TBD Discussions: TBD Goals: 1. Students will understand how genes and environments interact to produce phenotypes, including biological fitness, and influence which alleles are passed on to the next generation. 2. Mathematical models make our assumptions explicit. We will develop and apply simple mathematical models for studying evolution in natural populations. 3. Students will improve their ability to ask questions and answer them using scientific methods. 4. Students will gain factual knowledge of terms and concepts used to study evolution in natural populations. Instructors and their contact information. TBD Office hours are the best way to get help and feedback. If you have a complicated question, are struggling to understand something, or want to dive deeper, come to office hours of the professor or the GSI. Grade Breakdown Activity (see below for details) Points Discussion section quizzes (5 @ 2 pts.
[Show full text]
Role of Sexual Imprinting in Assortative Mating and Premating Isolation in Darwin’S Finches
Role of sexual imprinting in assortative mating and premating isolation in Darwin’s finches Peter R. Granta,1 and B. Rosemary Granta aDepartment of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544 Contributed by Peter R. Grant, September 11, 2018 (sent for review August 8, 2018; reviewed by Darren Irwin and Carel ten Cate) Global biodiversity is being degraded at an unprecedented rate, as shown by the numerous examples of introgressive hybridiza- so it is important to preserve the potential for future specia- tion between recently formed species (reviewed in refs. 10–13). tion. Providing for the future requires understanding speciation Important questions that need to be addressed are how the as a contemporary ecological process. Phylogenetically young barrier is constructed, how it evolved, why it occasionally leaks, adaptive radiations are a good choice for detailed study because and how gene exchange affects the evolution of the respective diversification is ongoing. A key question is how incipient species populations (14). Paradoxically, the breakdown of reproductive become reproductively isolated from each other. Barriers to gene isolation may be especially informative in answering questions exchange have been investigated experimentally in the laboratory about how it was established by exposing candidate traits that and in the field, but little information exists from the quantitative constitute the normally effective barrier to interbreeding (15– study of mating patterns in nature. Although the degree to which 17). Further insights can then be gained by conducting experi- genetic variation underlying mate-preference learning is un- ments on the genetic and experiential basis of mate choice and known, we provide evidence that two species of Darwin’s finches preferences of closely related species (16, 18–22).
[Show full text]
Ecological Genetics – HS18 V0.2 Gleb Ebert October 13, 2018
Ecological Genetics – HS18 v0.2 Gleb Ebert October 13, 2018 Vorwort This document aims to summarize the lecture Ecological Genetics as it was taught in the autumn semester of 2018. Unfortunately I can’t guarantee that it is complete and free of errors. You can contact me under [email protected] if you have any suggestions for improvement. The newest version of this summary can always be found here: https://n.ethz.ch/~glebert/ Contents 1 Introduction 2 2 Species 2 3 Molecular Markers 3 4 Sampling 4 1 1 Introduction 2.1 Species concepts • Morphological / typological species concept: focus on “Nothing in biology makes sense except in the light of similar morphology evolution” • Biological species concept: group of potentially or — Theodosius Dobzhansky actually interbreeding populations which are repro- ductively isolated from other such groups In 1971 Ford wrote that ecological genetics deal with the • Phylogenetic species concept: focuses on monophyletic adjustments and adaptations of wild populations to their lineages environment. According to Conner and Hartl (2004) eco- logical genetics is the study of the process of phenotypic 2.2 Operational Taxonomic Unit evolution occurring in present-day natural populations and is concerned with the genetics of ecologically important An OTU is a group of organisms that is treated as a distinct traits, that is, those traits related to ﬁtness. evolutionary unit for the purposes of research underway. Phenotypic evolution is the change in the mean or vari- They are often applied when one or several species con- ance of a trait across generations due to changes in allele cepts fail.
[Show full text]
The Ecological Genetics of Floral Traits
Heredity (2006) 97, 86–87 & 2006 Nature Publishing Group All rights reserved 0018-067X/06 $30.00 www.nature.com/hdy NEWS AND COMMENTARY ...............................................................Adaptive evolution zygomorphs does not represent a long- term constraint on angiosperm evolu- The ecological genetics of floral tion. Studies that focus on lineages with both actinomorphic and zygomorphic traits species could be useful in resolving this contradiction between patterns of CM Caruso genetic variation within species and ........................................................... speciation within clades. Heredity (2006) 97, 86–87. doi:10.1038/sj.hdy.6800853; published online 31 May 2006 Finally, mean rg between flower size and number was not significantly dif- ferent from zero, which does not sup- loral traits have fascinated evolu- because evolution in response to natural port the hypothesis that the evolution of tionary biologists since Darwin selection is slower for species with floral displays is genetically constrained F published ‘The various contri- lower h2, self-pollinating angiosperm by a trade-off between the size and vances by which orchids are fertilized species will not be able to respond to number of flowers produced by a plant. by insects’ in 1862. Because flowers are novel selection pressures and conse- This is a significant result because the remarkably diverse and important for quently may have elevated extinction inverse relationship between flower size sexual reproduction in plants, floral rates. The evolution of selfing species and number is the type of resource traits are excellent subjects for studies from outcrossing ancestors is one of the allocation trade-off that underlies much of adaptive microevolution. In addition, most common evolutionary transitions of life history and sex allocation theory floral traits are unique among plant in angiosperms and, as such, Stebbins’ and is an assumption of many theore- traits because they can directly influ- hypothesis has dominated the field of tical models of floral evolution.
[Show full text]
The Evolutionary Genetics of Adaptation: a Simulation Study
Genet. Res., Camb.(1999), 74, pp. 207–214. With 4 figures. Printed in the United Kingdom # 1999 Cambridge University Press 207 The evolutionary genetics of adaptation: a simulation study H.ALLEN ORR* Department of Biology, Uniersity of Rochester, Rochester, NY 14627, USA (Receied 30 March 1999 and in reised form 1 July 1999) Summary It is now clear that the genetic basis of adaptation does not resemble that assumed by the infinitesimal model. Instead, adaptation often involves a modest number of factors of large effect and a greater number of factors of smaller effect. After reviewing relevant experimental studies, I consider recent theoretical attempts to predict the genetic architecture of adaptation from first principles. In particular, I review the history of work on Fisher’s geometric model of adaptation, including recent studies which suggest that adaptation should be characterized by exponential distributions of gene effects. I also present the results of new simulation studies that test the robustness of this finding. I explore the effects of changes in the distribution of mutational effects (absolute versus relative) as well as in the nature of the character studied (total phenotypic effect versus single characters). The results show that adaptation towards a fixed optimum is generally characterized by an exponential effects trend. The situation to which these studies point is not one of a More recent work has confirmed these classic large number of genes all with more or less equal effect. It findings from ecological genetics. ffrench-Constant seems, rather, that a small number of genes with large effects (1994), for instance, has shown that insecticide are responsible for most of the response, the remainder of the response being due to a larger number of loci with small (cyclodiene) resistance in the wild among at least three effects.
[Show full text]
Recent Trends in Research on the Genetic Diversity of Plants: Implications for Conservation
diversity Article Recent Trends in Research on the Genetic Diversity of Plants: Implications for Conservation Yasmin G. S. Carvalho 1, Luciana C. Vitorino 1,* , Ueric J. B. de Souza 2,3 and Layara A. Bessa 1 1 Laboratory of Plant Mineral Nutrition, Instituto Federal Goiano campus Rio Verde, Rodovia Sul Goiana, km 01, Zona Rural, Rio Verde, GO 75901-970, Brazil; [email protected] (Y.G.S.C.); [email protected] (L.A.B.) 2 Laboratory of Genetics and Biodiversity, Instituto de Ciências Biológicas, Universidade Federal de Goiás—UFG, Avenida Esperança s/n, campus Samambaia, Goiânia, GO 74690-900, Brazil; [email protected] 3 National Institute for Science and Technology in Ecology, Evolution and Conservation of Biodiversity, Universidade Federal de Goiás, Goiânia, GO 74690-900, Brazil * Correspondence: [email protected] Received: 21 March 2019; Accepted: 16 April 2019; Published: 18 April 2019 Abstract: Genetic diversity and its distribution, both within and between populations, may be determined by micro-evolutionary processes, such as the demographic history of populations, natural selection, and gene ﬂow. In plants, indices of genetic diversity (e.g., k, h and π) and structure (e.g., FST) are typically inferred from sequences of chloroplast markers. Given the recent advances and popularization of molecular techniques for research in population genetics, phylogenetics, phylogeography, and ecology, we adopted a scientometric approach to compile evidence on the recent trends in the use of cpDNA sequences as markers for the analysis of genetic diversity in botanical studies, over the years. We also used phylogenetic modeling to assess the relative contribution of relatedness or ecological and reproductive characters to the genetic diversity of plants.
[Show full text]
Linking Ecological Divergence and Reproductive Isolation: a Tale of Two Killifish
LINKING ECOLOGICAL DIVERGENCE AND REPRODUCTIVE ISOLATION: A TALE OF TWO KILLIFISH BY EMMA LISBETH CORASH BERDAN DISSERTATION Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biology with a concentration in Ecology, Ethology, and Evolution in the Graduate College of the University of Illinois at Urbana-Champaign, 2012 Urbana, Illinois Doctoral Committee: Associate Professor Rebecca C. Fuller, Chair and Director of Research Professor Stewart Berlocher Associate Professor Chi-Hing Christina Cheng Assistant Professor Alison M. Bell ABSTRACT Gene flow and recombination directly oppose genetic differentiation and speciation because they homogenize allele combinations that are unique to each population/species (Felsenstein 1981; Rieseberg 2001; Ortiz-Barrientos, Reiland et al. 2002; Butlin 2005). Under divergence with gene flow, either very strong selection or some other mechanism that reduces recombination rates is needed to maintain different allelic combinations. Decreased recombination is especially important in cases of ecological speciation with gene flow. A decade of work in evolutionary biology indicates that divergent natural selection in different habitats is usually involved in speciation (i.e. ecological speciation). While ecological selection alone can promote speciation (Schluter 2001; Rundle and Nosil 2005; Schluter and Conte 2009), a variety of species contain populations that are adapted to different habitats and yet have not undergone speciation (Hendry 2009; Nosil, Harmon et al. 2009). These conflicting outcomes suggest that ecological selection need not always lead to the evolution of reproductive isolating barriers (RIBs). When the genes under ecological selection also confer reproductive isolation, ecological speciation occurs readily (Boughman 2001; Kirkpatrick and Ravigne 2002; Gavrilets 2004).
[Show full text]
The Rate of Spontaneous Mutation for Life-History Traits in Caenorhabditis Elegans
Copyright 1999 by the Genetics Society of America The Rate of Spontaneous Mutation for Life-History Traits in Caenorhabditis elegans Larissa L. Vassilieva and Michael Lynch Department of Biology, University of Oregon, Eugene, Oregon 97403 Manuscript received September 1, 1997 Accepted for publication September 18, 1998 ABSTRACT Spontaneous mutations were accumulated in 100 replicate lines of Caenorhabditis elegans over a period of z50 generations. Periodic assays of these lines and comparison to a frozen control suggest that the deleterious mutation rate for typical life-history characters in this species is at least 0.05 per diploid genome per generation, with the average mutational effect on the order of 14% or less in the homozygous state and the average mutational heritability z0.0034. While the average mutation rate per character and the average mutational heritability for this species are somewhat lower than previous estimates for Drosophila, these differences can be reconciled to a large extent when the biological differences between these species are taken into consideration. RACTICAL interest in the properties of new muta- relevance to the adaptive evolutionary process is far Ptions is motivated by two issues. First, the viability of from clear. Although the data are taxonomically limited, species con®ned to a temporally changing environment the existing evidence for Drosophila and Escherichia coli ultimately depends on the rate at which mutation can imply that the vast majority of mutations have deleteri- generate new variation that can be assimilated into the ous effects on ®tness (Simmons and Crow 1977; Crow adaptive evolutionary process (Lynch and Lande 1993; and Simmons 1983; Crow 1993; Houle et al.
[Show full text]
Evolutionary and Ecological Genetics of Medicago Truncatula
Medicago truncatula handbook version November 2006 Evolutionary and Ecological Genetics of Medicago truncatula Thomas Bataillon Bioinformatics Research Center & Department of Genetics and Ecology, Aarhus University, Hoegh-Guldbergs Gade 10, Building 1090, DK-8000 Aarhus C. Denmark [email protected] http://www.daimi.au.dk/~tbata Joelle Ronfort UMR 1097 DGPC, INRA domaine de Melgueil, F-34130 Maugio, France. [email protected] Table of contents 1. Introduction 2. The mating system of Medicago truncatula 3. Distribution of genetic variation in Medicago truncatula 3.1 Within population polymorphism 3.2 Population structure in Medicago truncatula 4. Variation in quantitative traits: Is there ecotypic differentiation in Medicago truncatula? 5 Perspectives: towards the ecological and evolutionary genomics of Medicago truncatula References Figures Abstract This chapter synthesizes our current knowledge on the ecological genetics of the model legume Medicago truncatula. After a short introduction to the life cycle of the species, we describe the mating system of M truncatula and how selfing rates in nature can be inferred both by progeny testing and population surveys. We then review what is currently known on the distribution of genetic diversity within and among populations focusing first on the diversity that can be assessed using a priori neutral makers (allozyme and SSR). We then consider genetic variation for quantitative traits and discuss whether Medicago truncatula exhibits a so called “ecotypic” differentiation. Last we discuss how genomic tools and the availability of sequence information may help shed additional light on the evolutionary forces behind evolution and adaptation in Medicago truncatula. Evolutionary and Ecological Genetics of Medicago truncatula Page 1 of 13 Medicago truncatula handbook version November 2006 1 Introduction Medicago truncatula GAERTN is an annual species which is strongly selfing in nature.
[Show full text]
Biology B242: Evolutionary and Ecological Genetics
BIOLOGY B242: EVOLUTIONARY AND ECOLOGICAL GENETICS EXAM 2001 Answer ONE question from section A, TWO questions from section B, and ALL OF section C (overleaf). Each section carries 1/3 of the marks on the paper. SECTION A. Answer ONE of questions 1-3. 1. Why is heritability useful and how do we estimate it? Discuss some examples of its application in evolution. 2. Write an essay on recent theories and evidence from natural populations that address the problem of sympatric speciation. 3. Why has sex evolved? SECTION B. Answer TWO of questions 4-8. 4. “When animals interact, they play games”. Discuss and justify. 5. How does Darwin’s theory rely on Mendel’s mechanism? 6. Describe the key features of “balancer chromosomes”, and explain their usefulness in the study of mutation. 7. Why, in the animals, do males tend to be more elaborately ornamented than females? 8. What use is the “Hardy-Weinberg equilibrium” in modern evolutionary genetics? Remember to answer Section C overleaf! TURN OVER SECTION C. Attempt ALL parts of question 9. 9. Cystic fibrosis (CF) is a single-locus recessive genetic disease of humans. The gene is on chromosome 7, and affected individuals in Scotland occur at a frequency of 1 in 1,984 newborns: it is one of the commonest serious genetic diseases among Europeans. Affected individuals rarely survive to reproduce. a) Assuming random mating with respect to this gene, what is the frequency of mutant CF alleles in the Scottish population? b) Assuming random mating, what is the frequency of carriers (i.e.
[Show full text]